Hydrodynamic effects in the capture of rod-like molecules by a nanopore

TL;DR

This paper provides a detailed theoretical analysis of how hydrodynamic anisotropy and near-wall interactions influence the capture and approach dynamics of rod-like biomolecules by nanopores, highlighting the importance of these effects in modeling.

Contribution

It introduces a comprehensive theoretical framework for understanding hydrodynamic effects on rod-like molecules near nanopores, including trajectory analysis and the impact of boundary shape.

Findings

Brownian motion negligible within pore capture radius

Hydrodynamic interactions shape approach trajectories

Anisotropic mobility significantly affects molecule capture dynamics

Abstract

In the approach of biomolecules to a nanopore, it is essential to capture the effects of hydrodynamic anisotropy of the molecules and the near-wall hydrodynamic interactions which hinder their diffusion. We present a detailed theoretical analysis of the behaviour of a rod-like molecule attracted electrostatically by a charged nanopore. We first estimate the time scales corresponding to Brownian and electrostatic translations and reorientation. We find that Brownian motion becomes negligible at distances within the pore capture radius, and numerically determine the trajectories of the nano-rod in this region to explore the effects of anisotropic mobility. This allows us to determine the range of directions from the pore in which hydrodynamic interactions with the boundary shape the approach dynamics and need to be accounted for in detailed modelling.